Potential Roles for Ubiquitin and the Proteasome during Ribosome Biogenesis

Abstract

We have investigated the possible involvement of the ubiquitin-proteasome system (UPS) in ribosome biogenesis. We find by immunofluorescence that ubiquitin is present within nucleoli and also demonstrate by immunoprecipitation that complexes associated with pre-rRNA processing factors are ubiquitinated. Using short proteasome inhibition treatments, we show by fluorescence microscopy that nucleolar morphology is disrupted for some but not all factors involved in ribosome biogenesis. Interference with proteasome degradation also induces the accumulation of 90S preribosomes, alters the dynamic properties of a number of processing factors, slows the release of mature rRNA from the nucleolus, and leads to the depletion of 18S and 28S rRNAs. Together, these results suggest that the UPS is probably involved at many steps during ribosome biogenesis, including the maturation of the 90S preribosome.The nucleolus serves many functions (4, 23, 36, 51); however, its most prominent function remains ribosome biogenesis. This process comprises rRNA gene transcription; processing of the 47S pre-rRNA to mature 18S, 5.8S, and 28S rRNAs; and assembly of preribosomal particles (21). Ribosome biogenesis is spatially organized in distinct compartments within the nucleolus. Transcriptionally active ribosomal genes are thought to be situated at either the boundaries of the fibrillar centers (FCs) and dense fibrillar components (DFCs) or in DFCs (45), whereas both the pre-rRNA processing and the assembly of preribosomal particles occur in the DFCs and granular components (GCs) (46). Ribosome biogenesis is regulated at multiple levels, including the transcription of ribosomal genes and the phosphorylation, methylation, and acetylation of component nucleolar factors, plus the trafficking and interaction of these factors (30).Proteasomal regulation has been implicated in many processes, including cell cycle progression, transcription, and antigen processing (24) (18,34,58). Indirect evidence has hinted at a possible role for the ubiquitin-proteasome system (UPS) in ribosomal biogenesis. Two different ubiquitination patterns have been reported for the late processing factor B23 (25,48). Several other ribosomal factors may be ubiquitinated, as suggested by a recent proteomic analysis in yeast (37). It has also been known for many years that two ubiquitin precursors are ribosomal fusion proteins (5,16,47). A large ribosomal subunit protein (L28) forms the most abundant ubiquitin-protein conjugate in yeast, and this modification is essential for ribosome function and efficient translation (53). A possible role for ubiquitin in nucleolus disassembly was also suggested (54). In addition, a ubiquitin ligase is known to regulate the processing and nuclear export of rRNA, as well as tRNA and mRNA in yeast (35). Finally, a temperature-sensitive point mutation of the Cic1p/Nsa3p yeast protein, an adaptor for the 26S proteasome, associates with early pre-60S particles (49), and inhibits both the synthesis of the mature 5.8S and 25S rRNAs and the releas...

Characterization of a Short Isoform of Human Tgs1 Hypermethylase Associating with Small Nucleolar Ribonucleoprotein Core Proteins and Produced by Limited Proteolytic Processing

“…Its accumulation in Cajal bodies following proteasome inhibition (Fig. 8B) is consistent with a recent study reporting that MG132 treatment modulates the relative distributions of various nucleolar proteins, such as the snoRNPs core proteins fibrillarin and Nop58 (41). It also alters their nuclear distribution, since Nop58 becomes localized in Cajal bodies (41).…”

“…8B) is consistent with a recent study reporting that MG132 treatment modulates the relative distributions of various nucleolar proteins, such as the snoRNPs core proteins fibrillarin and Nop58 (41). It also alters their nuclear distribution, since Nop58 becomes localized in Cajal bodies (41). In addition to its effect on the distribution of early processing factors, proteasome inhibition also results in a decrease in rRNA gene transcription as well as rRNA production.…”

“…In addition to its effect on the distribution of early processing factors, proteasome inhibition also results in a decrease in rRNA gene transcription as well as rRNA production. Thus, the proteasomal system has been shown to be involved in multiple steps of ribosome biogenesis (41).…”

A Mutant Plasma Membrane Protein Is Stabilized Upon Loss of Yvh1, a Novel Ribosome Assembly Factor

“…Yvh1 phosphatase activity has been demonstrated in vitro (Guan et al 1992), and we can speculate that Yvh1 phosphatase activity may have a regulatory function in vivo that affects ribosomal assembly and perhaps synthesis of specific proteins under certain conditions. The ubiquitin-proteasome system also participates in ribosome biogenesis (Kim et al 2006;Stavrena et al 2006). Although many ubiquitin ligases have RING finger domains (Fang et al 2003), there is no evidence at present for a role for Yvh1 in ubiquitination: no significant difference in the profile of ubiquitinated proteins was observed in wild-type and yvh1D cells ( Figure 2C).…”

The PML nuclear bodies-associated protein TTRAP regulates ribosome biogenesis in nucleolar cavities upon proteasome inhibition

“…18 It is subjected to stringent quality control mechanisms 19,20 and stressful events elicit homeostatic responses that involve the majority of its steps. 21,22 Several human genetic diseases, collectively defined as ribosomopathies, are caused by mutations in genes that affect rRNA biogenesis and ribosome assembly. Congenital mutations in RPS19 and other genes encoding ribosomal proteins have been linked to Diamond-Blackfan anemia, a disorder characterized by a reduction of erythroid precursors.…”